Exploring signature multiplicity in microarray data using ensembles of randomized trees

A challenging and novel direction for feature selection research in computational biology is the analysis of signature multiplicity. In this work, we propose to investigate the eect of signature multiplicity on feature importance scores derived from tree-based ensemble methods. We show that looking at individual tree rankings in an ensemble could highlight the existence of multiple signatures and we propose a simple post-processing method based on clustering that can return smaller signatures with better predictive performance than signatures derived from the global tree ranking at almost no additional cost

Detecting adversarial examples with inductive Venn-ABERS predictors

Inductive Venn-ABERS predictors (IVAPs) are a type of probabilistic predictors with the theoretical guarantee that their predictions are perfectly calibrated. We propose to exploit this calibration property for the detection of adversarial examples in binary classification tasks. By rejecting predictions if the uncertainty of the IVAP is too high, we obtain an algorithm that is both accurate on the original test set and significantly more robust to adversarial examples. The method appears to be competitive to the state of the art in adversarial defense, both in terms of robustness as well as scalabilit

Detecting adversarial manipulation using inductive Venn-ABERS predictors

Inductive Venn-ABERS predictors (IVAPs) are a type of probabilistic predictors with the theoretical guarantee that their predictions are perfectly calibrated. In this paper, we propose to exploit this calibration property for the detection of adversarial examples in binary classification tasks. By rejecting predictions if the uncertainty of the IVAP is too high, we obtain an algorithm that is both accurate on the original test set and resistant to adversarial examples. This robustness is observed on adversarials for the underlying model as well as adversarials that were generated by taking the IVAP into account. The method appears to offer competitive robustness compared to the state-of-the-art in adversarial defense yet it is computationally much more tractable

Netter: re-ranking gene network inference predictions using structural network properties

Background: Many algorithms have been developed to infer the topology of gene regulatory networks from gene expression data. These methods typically produce a ranking of links between genes with associated confidence scores, after which a certain threshold is chosen to produce the inferred topology. However, the structural properties of the predicted network do not resemble those typical for a gene regulatory network, as most algorithms only take into account connections found in the data and do not include known graph properties in their inference process. This lowers the prediction accuracy of these methods, limiting their usability in practice. Results: We propose a post-processing algorithm which is applicable to any confidence ranking of regulatory interactions obtained from a network inference method which can use, inter alia, graphlets and several graph-invariant properties to re-rank the links into a more accurate prediction. To demonstrate the potential of our approach, we re-rank predictions of six different state-of-the-art algorithms using three simple network properties as optimization criteria and show that Netter can improve the predictions made on both artificially generated data as well as the DREAM4 and DREAM5 benchmarks. Additionally, the DREAM5 E. coli. community prediction inferred from real expression data is further improved. Furthermore, Netter compares favorably to other post-processing algorithms and is not restricted to correlation-like predictions. Lastly, we demonstrate that the performance increase is robust for a wide range of parameter settings. Netter is available at http://bioinformatics. intec. ugent. be. Conclusions: Network inference from high-throughput data is a long-standing challenge. In this work, we present Netter, which can further refine network predictions based on a set of user-defined graph properties. Netter is a flexible system which can be applied in unison with any method producing a ranking from omics data. It can be tailored to specific prior knowledge by expert users but can also be applied in general uses cases. Concluding, we believe that Netter is an interesting second step in the network inference process to further increase the quality of prediction

Java-ML: a machine learning library

Java-ML is a collection of machine learning and data mining algorithms, which aims to be a readily usable and easily extensible API for both software developers and research scientists. The interfaces for each type of algorithm are kept simple and algorithms strictly follow their respective interface. Comparing different classifiers or clustering algorithms is therefore straightforward, and implementing new algorithms is also easy. The implementations of the algorithms are clearly written, properly documented and can thus be used as a reference. The library is written in Java and is available from http://java-ml.sourceforge.net/ under the GNU GPL license